Contacts of the helix formed by residues 33 - 42 (chain E) in PDB entry 5K58
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 33 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG* 3.4 17.2 + - + +
32E ILE* 1.3 75.6 - - - +
34E THR* 1.3 58.7 + - - +
35E ALA* 3.5 9.3 + - - +
36E LYS* 3.1 43.7 + - + +
37E LEU* 3.0 30.5 + - - +
55E LYS* 4.4 1.3 - - - -
6T G 4.1 9.1 - - - +
7T T 4.0 21.1 - - - +
8T A 3.5 20.9 - - - +
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Residues in contact with THR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E THR* 1.3 71.6 - - - +
35E ALA* 1.3 69.3 + - - +
37E LEU* 3.4 6.9 + - + +
38E ALA* 3.2 21.7 + - - +
45E GLU* 2.6 32.4 + - - +
48E LEU* 4.4 10.5 - - + +
49E TYR* 3.9 13.7 - - + +
55E LYS* 4.3 11.0 - - + +
8T A 3.1 56.3 + - + +
9T C 4.4 5.2 - - + +
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Residues in contact with ALA 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E THR* 3.6 9.1 - - - +
34E THR* 1.3 84.8 + - - +
36E LYS* 1.3 64.8 + - + +
38E ALA* 3.3 11.8 + - - +
39E ALA* 3.4 9.4 + - - +
45E GLU* 3.6 24.0 - - - +
6T G 6.0 5.8 - - - -
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Residues in contact with LYS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E MET* 3.7 24.5 - - + +
27E ASP* 5.8 11.6 + - + +
30E GLN* 5.5 7.9 - - - +
31E ARG 4.9 7.7 + - - +
32E ILE* 5.9 0.7 - - - -
33E THR* 3.1 33.8 + - + +
35E ALA* 1.3 79.9 - - + +
37E LEU* 1.3 64.9 + - - +
39E ALA* 3.1 23.7 + - + +
40E SER 3.6 4.3 + - - -
6T G 6.4 2.7 - - - -
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Residues in contact with LEU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 4.2 13.7 - - + +
18E SER* 4.7 3.4 - - - -
19E LEU* 4.1 38.8 - - + +
22E MET* 4.0 14.1 - - - -
32E ILE* 4.5 13.0 - - + -
33E THR 3.0 20.5 + - - +
34E THR* 3.8 7.0 - - + +
35E ALA 3.3 0.2 - - - -
36E LYS* 1.3 77.0 - - - +
38E ALA* 1.3 61.0 + - - +
39E ALA 3.5 0.2 + - - -
40E SER* 3.6 6.9 + - - -
41E VAL* 3.5 15.3 + - - +
48E LEU* 3.9 14.4 - - + -
55E LYS* 4.7 10.8 - - + -
58E MET* 3.7 31.4 - - + -
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E THR 3.2 12.1 + - - +
35E ALA 3.5 10.3 - - - +
36E LYS 3.2 0.2 - - - -
37E LEU* 1.3 76.7 - - - +
39E ALA* 1.3 52.7 + - - +
40E SER 3.2 0.2 + - - -
41E VAL* 3.2 1.9 + - - +
42E GLY* 2.5 37.5 + - - -
43E VAL* 3.4 21.2 + - - +
44E SER 4.0 4.3 - - - +
45E GLU* 4.0 22.2 - - + +
48E LEU* 4.4 10.9 - - + +
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ALA 3.4 5.2 + - - +
36E LYS* 3.1 20.3 + - + +
38E ALA* 1.3 79.9 - - - +
40E SER* 1.3 62.1 + - - +
42E GLY* 3.6 9.4 + - - +
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Residues in contact with SER 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E SER* 3.0 37.3 + - - -
21E LEU* 4.3 13.7 - - - +
22E MET* 4.8 11.6 - - - +
36E LYS 3.6 4.5 + - - -
37E LEU 3.6 7.9 + - - -
38E ALA 3.2 0.4 - - - -
39E ALA* 1.3 78.2 - - - +
41E VAL* 1.3 64.9 + - - +
42E GLY* 3.4 0.5 + - - -
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Residues in contact with VAL 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLU* 5.3 4.3 - - + +
15E ILE* 3.9 39.5 - - + -
18E SER* 3.9 20.6 - - - +
37E LEU 3.5 16.8 - - - +
38E ALA* 3.2 1.7 + - - +
40E SER* 1.3 75.2 - - - +
42E GLY* 1.3 59.3 + - - +
43E VAL* 3.2 34.3 + - + +
48E LEU* 4.8 1.6 - - + -
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Residues in contact with GLY 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA 2.5 16.9 + - - -
39E ALA* 3.9 9.2 - - - -
40E SER 3.2 2.9 - - - -
41E VAL* 1.3 73.2 - - - +
43E VAL* 1.3 62.4 + - - +
3R T 4.9 2.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il